The results of monitoring over the years have shown that the mixing and coexistence of various low-level antibiotic residual pollutants has increased significantly, among which, the problems of enrofloxacin (ENR) and ciprofloxacin (CIP) were more prominent. At present, research studies on the metabolism of ENR or CIP are focused on the individual drugs, and there is no relevant research reporting on the effect of the combination of the two antibiotics on the metabolism of ENR. This research study evaluated the effect of CIP on ENR metabolism in pigs and its mechanism in vivo and in vitro. The results showed that CIP changed the pharmacokinetics of ENR through the inhibition of CYP3A29 and the “steric-like effect” of ENR binding to CYP3A29, which increased the residual concentration of ENR in pigs, a result that requires an extension of the withdrawal period. In order to ensure human health, the combined use of these two drugs, CIP and ENR, must be avoided in veterinary medicine in food producing animals.